[galaxy-dev] protein ligand docking

Dear list, I have recently evaluated the software for protein docking that is available in the toolshed. I could need some help / suggestions. 1. autodock_vina The receptor of my example contains Au atoms which are not understood by autodock_vina. For autodock there is the possibility to

Re: [galaxy-dev] python subprocess OSError when running bwa-mem

Hi run.sh On 05/24/2017 10:51 AM, Georgios Nikolis wrote: Hi Hans-Rudolf, many thanks for pointing me to the right direction. samtools was installed, it was indeed a problem with $PATH. There are actually path setting scripts provides with the tools, also for samtools, e.g.

Re: [galaxy-dev] python subprocess OSError when running bwa-mem

Hi Hans-Rudolf, many thanks for pointing me to the right direction. samtools was installed, it was indeed a problem with $PATH. There are actually path setting scripts provides with the tools, also for samtools, e.g.

Re: [galaxy-dev] Decrease Galaxy polling of slurm?

Thanks Nate! I have no idea if this is actually having any impact, but keeping admins happy is of utmost importance. :-) Phil On Wed, May 24, 2017 at 8:58 AM, Nate Coraor wrote: > Hi Phil, > > Unfortunately, there's no configurable for this. You can, however, modify > the

Re: [galaxy-dev] Decrease Galaxy polling of slurm?

Hi Phil, Unfortunately, there's no configurable for this. You can, however, modify the loop's sleep here: https://github.com/galaxyproject/galaxy/blob/d7a0fdfaa748ca427dda1cef74b81e253f1921d5/lib/galaxy/jobs/runners/__init__.py#L552 Hope this helps, --nate On Wed, May 24, 2017 at 10:40 AM,

[galaxy-dev] Decrease Galaxy polling of slurm?

An admin at our center noticed our Galaxy instance is polling slurm every second and asked if the polling frequency can be decreased. Is there an easy way to do this? Phil -- Philip D. Blood, Ph.D. Senior Computational Scientist Voice: (412) 268-9329 Pittsburgh Supercomputing Center

[galaxy-dev] vcftools - errors running vcf-merge

Hi all, I am trying to run the vcf-merge tool, which depends on the vcftools 0.1.11 package. I have this vcftools package and also the required tabix 0.2.6 both installed via the toolshed (tabix is set in the PATH of the Galaxy startup script). However, I keep getting gunzip error messages